\chapter{Analysis}

\section{``On-the-fly'' analysis in Brahms}

Most properties of interest can be calculated and averaged by \brahms while the simulation is running (``on-the-fly'' analysis). \brahms analysis options can be controlled via the input file {\tt brahms.an}, described in detail in \textsection\ref{sec:brahms.an}.
Examples of \brahms analysis results can be seen in Figures~2-5 of Orsi et al;~\cite{marioDmpcDopc} in particular, these curves were obtained from the averages taken over all profiles periodically outputted by Brahms. To carry out such analysis it is possible to use the script {\tt getAverageProfile.py} located in the {\tt analysisScripts/general/} directory (read first comment lines for usage instructions).


\section{Post-processing analysis}

Not all the possible analysis of simulation data is carried out ``on-the-fly''. In some cases it is better to output data files for post-processing. Such post-processing can be done through simple Python scripts or command line instructions; such tools are collected in the directory {\tt analysisScripts}.
For example, compressibility moduli are most conveniently obtained via post-processing (see \textsection\ref{sec:regDims}); nice images produced with simple post-processing can be seen in Figure~6 of Orsi et al.~\cite{marioDmpcDopc} (see \textsection\ref{sec:lld} for suggestions on how to reproduce such plots).
